get.scc {hicrep}R Documentation

calculate the stratum-adjusted correlation coefficient

Description

calculate the stratum-adjusted correlation coefficient

Usage

get.scc(dat, resol, max)

Arguments

dat

A matrix of four columns. The first two are the mid-point coordinates of two interacting bin.

resol

An integer indicating the resolution of the Hi-C matrix.

max

An integer indicating the maximum distance of interaction that is considered.

Details

The function stratifies the Hi-C reads count according to their interacting distance, calculates the Pearson correlation coefficient for each stratum, then aggregrates them using a weighted average.

Value

A list of results including stratum-specific correlation coefficients, weights, stratum-adjusted correlation coefficient (scc), and the asymptotic standard deviation of scc.

References

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient. Tao Yang, Feipeng Zhang, Galip Gurkan Yardimci, Ross C Hardison, William Stafford Noble, Feng Yue, Qunhua Li. bioRxiv 101386; doi: https://doi.org/10.1101/101386.

Examples

data(HiCR1)
data(HiCR2)
processed <- prep(HiCR1, HiCR2, 1000000, 0, 5000000)

scc.out = get.scc(processed, 1000000, 5000000)
scc.out$scc
scc.out$std

[Package hicrep version 1.10.0 Index]